sliding.window.transform-methods | R Documentation |
This generic function transforms an existing object of class "GENOME"
into another object of class "GENOME"
,
in which each region corresponds to one window. This allows to apply the full spectrum of PopGenome methods to
sliding window data.
## S4 method for signature 'GENOME'
sliding.window.transform(object,
width=7, jump=5,
type=1,
start.pos=FALSE,end.pos=FALSE,
whole.data=TRUE
)
object |
an object of class |
width |
window size. default: |
jump |
jump size. default: |
type |
|
start.pos |
start position |
end.pos |
end position |
whole.data |
scan the complete data by concatenating the regions in "object". If FALSE, each region is scanned seperately. |
The function creates a transformed object of class "GENOME"
.
If you want to scan regions seperately (whole.data=FALSE), you may not use the big.data option in the readData function. PopGenome will scan the data from position 1 to the last observed SNP if start or end-positions are not specified.
# GENOME.class <- readData("...\Alignments")
# slide.GENOME.class <- sliding.window.transform(GENOME.class)
# slide.GENOME.class <- sliding.window.transform(GENOME.class,100,100)
# slide.GENOME.class <- neutrality.stats(slide.GENOME.class)
# slide.GENOME.class@region.names
# values <- get.neutrality(slide.GENOME.class)
# GENOME.class <- readSNP("Arabidopsis", CHR=1)
# GENOME.slide <- sliding.window.transform(GENOME.split, 10000, 10000, type=2,
# start.pos=10000000, end.pos=12000000)
# GENOME.slide@region.names
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